Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Caulo:CCNA_03695 Length = 506 Score = 294 bits (753), Expect = 4e-84 Identities = 166/463 (35%), Positives = 256/463 (55%), Gaps = 15/463 (3%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 +P G + EIA + A ++ A+ AA AA A W +T+ R+ LL++AD +EEN A Sbjct: 40 SPIHGRKICEIARSQAIDIERALDAAHAAKAGWARTSAADRSRILLRIADRMEENLAALA 99 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVV 142 E+ + GKP+ +IP +D FR+FAG R G + E + +PLGVV Sbjct: 100 TAETWDNGKPIRETLAADIPLAIDHFRYFAGCLRSQEG-SISEIDHDTIAYHFHEPLGVV 158 Query: 143 ASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILFG 202 I PWN+PL+MA WKLAPALAAGNCVVLKP+E TP + + AE+ D+ PAGV+NI+ G Sbjct: 159 GQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASIMVWAEMIGDLLPAGVLNIVNG 218 Query: 203 RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVFDDAD-- 260 G G PL P++ ++ TG +TG I+ + A ++ +ELGGK+P I FDD Sbjct: 219 FGLEAGKPLASSPRIAKIAFTGETSTGRLIMQYAAQNLIPVTLELGGKSPNIFFDDVARE 278 Query: 261 ----IEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316 ++ +EG F N G+ CT R Q+ IY+ +E+ V + G+P D + Sbjct: 279 DDDYLDKALEGFTMFA-LNQGEVCTCPSRALVQESIYEKFMERALKRVNAVVQGSPLDPA 337 Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKR-----KGNGYYYAPTLLAGALQD 371 T +G +S L ++ ++ + G K++ GG+++ +GYY PT+ G Sbjct: 338 TMIGAQASEEQLNKILGYMDIGRNEG-AKLLAGGQRKILPGQLADGYYVEPTVFEGH-NK 395 Query: 372 DAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTW 431 I Q+E+FGPV++VT F EE+ + AND+ +GL + VW++D R +R ++ G W Sbjct: 396 MRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGAGVWSRDANRCYRFGRGIEAGRVW 455 Query: 432 VNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 N + + GG K SG G++ L+ Y ++++V + Sbjct: 456 TNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHYQQTKNMLVSY 498 Lambda K H 0.317 0.134 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 558 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 474 Length of database: 506 Length adjustment: 34 Effective length of query: 440 Effective length of database: 472 Effective search space: 207680 Effective search space used: 207680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory